From a47c5775c5edb21c0e98d4da04fbed61546141c8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 1 Feb 2024 17:32:13 +0100 Subject: [PATCH 1/4] Add warning if no GTDB results because no contigs pass filter --- subworkflows/local/gtdbtk.nf | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf index 370f3c4f..a201e370 100644 --- a/subworkflows/local/gtdbtk.nf +++ b/subworkflows/local/gtdbtk.nf @@ -77,6 +77,13 @@ workflow GTDBTK { error("Unsupported object given to --gtdb, database must be supplied as either a directory or a .tar.gz file!") } + + // Print warning why GTDB-TK summary empty if passed channel gets no files + ch_filtered_bins.passed + .count() + .map{it == 0 ? log.warn("No contigs passed GTDB-TK min. completeness filters. GTDB-TK summary will execute but results will be empty!") : ""} + + GTDBTK_CLASSIFYWF ( ch_filtered_bins.passed.groupTuple(), ch_db_for_gtdbtk, From 2c1274be3fc779fbfb1bd9ca9314e2ed2e91165e Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 1 Feb 2024 17:38:40 +0100 Subject: [PATCH 2/4] Add changelog and missing changelog entry --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5f38fcfe..152dffb1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- [#548](https://github.com/nf-core/mag/pull/548) fixes to GTDBK-TK execusion, CAT/QUAST/DEPTH bin summary file name collisions, BUSCO database parsing, correct CAT name files (reported by @maxibor, @PPpissar, @muniheart, @llborcard, fix by @maxibor) +- [#564](https://github.com/nf-core/mag/pull/558) - Add warning of empty GTDB-TK results if no contigs pass completeness filter (fix by @jfy133 and @maxibor) + ### `Changed` ### `Fixed` From dabc167ccdc37b539963046bffeb7c27e8a46d66 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 1 Feb 2024 20:45:19 +0100 Subject: [PATCH 3/4] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 152dffb1..291374d0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#548](https://github.com/nf-core/mag/pull/548) fixes to GTDBK-TK execusion, CAT/QUAST/DEPTH bin summary file name collisions, BUSCO database parsing, correct CAT name files (reported by @maxibor, @PPpissar, @muniheart, @llborcard, fix by @maxibor) -- [#564](https://github.com/nf-core/mag/pull/558) - Add warning of empty GTDB-TK results if no contigs pass completeness filter (fix by @jfy133 and @maxibor) +- [#565](https://github.com/nf-core/mag/pull/565) - Add warning of empty GTDB-TK results if no contigs pass completeness filter (fix by @jfy133 and @maxibor) ### `Changed` From 3ca1229fadda230029d8afb1f2a14819be229ca1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 1 Feb 2024 19:59:02 +0000 Subject: [PATCH 4/4] [automated] Fix linting with Prettier --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f240ea0f..16bb2293 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,10 +8,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#548](https://github.com/nf-core/mag/pull/548) - Fixes to (reported by @maxibor, @PPpissar, @muniheart, @llborcard, fix by @maxibor) - - GTDBK-TK execution + - GTDBK-TK execution - CAT/QUAST/DEPTH bin summary file name collisions - BUSCO database parsing - - Correct CAT name files + - Correct CAT name files - [#562](https://github.com/nf-core/mag/pull/562) - Add CAT summary into the global bin_summary (by @maxibor) - [#565](https://github.com/nf-core/mag/pull/565) - Add warning of empty GTDB-TK results if no contigs pass completeness filter (fix by @jfy133 and @maxibor)